If you've ever been to an air show, you've seen warbirds--P-51s, B-17s, B-24s--that we all marvel at. So few of them around, we are told. True enough. But decades ago, there were umpteen gazillion such planes. Now look. After WWII the planes were sent to the scrap heaps and our aviation heritage went with them.

Is that the fate of the airliners now in the desert? I don't advocate saving them all. That's silly. But surely there should be ways of saving the ones worth saving. Here at the Manchester (NH) Airport, we've just opened a gorgeous, new aviation museum celebrating New Hampshire aviation. Would we love to have a United Airlines 757 parked next to it? Sure! Who wouldn't? So what stands in the way, besides money, of doing that? Maybe it IS 'just money.' But it seems to me that this mass exodus of 'planes to the desert' is a great opportunity to SAVE some of those airframes to celebrate our heritage. I'm not talking about planes that are still being paid for; I'm talking about planes that are just done doing their job...forever. And instead of flying that jet to the desert, the carrier flies it to the 'Charity of their choice.' That seems to make sense to me, so does it ever work out that way?

Although one would like to preserve at least one example of every aircraft ever built, it does become a problem of $$$. When a bird has been described as "scrapped", it conjurs up a vision of the aircraft being wantonly destroyed. What actually happens is that the airframe is "dismantled and recycled" and as such, has value to those in that business, who pay $$$ for the salvage rights. To procure an airframe for preservation/restoration, one (or an organization) would have to bid for the salvage rights along with those engaged in the business. As many in the automotive business know, the sum of the parts that make up a vehicle outvalue the whole vehicle 100 fold. So an airframe WFU,stored, and valued as salvage/scrap, may have a value nearly equalling the in service airframe.

Saving big objects is problem because you can't always get them for a symbolic amount (large items are often build for making money and recycling is the final way to make at least a small profit) and keeping them in a proper (what ever that means?) state for the future will be costly as well.
Stored items most not loose to much of their value, so they must be maintained and that means space, people and money.

E.g. Imagine creating a Supertanker museum. That would indicate many of the problems saving big items: money, people, space, maintenance...
I think that we should be glad that a lot of airplanes still exist on museums. I do not think we will ever find a good balance, when it comes to which planes to save and not. But using a camera in one way of keeping parts of an item for the future. Interviews with the people that made and used it is worth doing - and not extremely expensive.

Personally I do feel that one of the biggest losses we have experience when it comes to airliners is the loss of the DC-9 prototype

Actually, there are very few commerical airliner models that have any historic value. Those that do would include the Comet Mk.I, B-707-100, B-747-100, Concorde, and maybe the A-300-B2 for jet aircraft. The pistons would include the Boeing Flying Boat, the L-749, DC-3, B-303 or B-377 and the B-247.

But, generally, commerical airliners do not inspire technological advancements, like military aircraft do. Additionally, military airplanes represent historic conflicts, in some cases globally, like WWII aircraft do. The advancement in aviation technoligy during war times, by both friends and foes, do have an impact on later designs, both military and commerical.